From: ericonr <ericonr@users.noreply.github.com>
To: ml@inbox.vuxu.org
Subject: [PR PATCH] pymol: enable for musl, fix byte-compilation.
Date: Mon, 28 Sep 2020 22:08:36 +0200 [thread overview]
Message-ID: <gh-mailinglist-notifications-41a7ca26-5023-4802-975b-f1789d68868e-void-packages-25162@inbox.vuxu.org> (raw)
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There is a new pull request by ericonr against master on the void-packages repository
https://github.com/ericonr/void-packages pymol
https://github.com/void-linux/void-packages/pull/25162
pymol: enable for musl, fix byte-compilation.
It doesn't segfault anymore :D
However, it's doing something weird in linking:
```
$ pymol
Traceback (most recent call last):
File "/usr/lib/python3.8/site-packages/pymol/__init__.py", line 64, in <module>
import pymol
File "/usr/lib/python3.8/site-packages/pymol/__init__.py", line 580, in <module>
import pymol._cmd
ImportError: Error relocating /usr/lib/python3.8/site-packages/pymol/_cmd.so: backtrace_symbols: symbol not found
$ LD_PRELOAD=/lib/libexecinfo.so.1 pymol
PyMOL(TM) Molecular Graphics System, Version 2.3.0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
[...]
```
It found the symbol while linking (I guess?) but it somehow wasn't recorded.
A patch file from https://github.com/void-linux/void-packages/pull/25162.patch is attached
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From fb51ebb5712773be5d16d5e7feb12f4000dc8e0a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=89rico=20Rolim?= <erico.erc@gmail.com>
Date: Mon, 28 Sep 2020 17:03:36 -0300
Subject: [PATCH] pymol: enable for musl, fix byte-compilation.
---
srcpkgs/pymol/patches/musl.patch | 13 +++++++++++++
srcpkgs/pymol/template | 12 ++++++++----
2 files changed, 21 insertions(+), 4 deletions(-)
create mode 100644 srcpkgs/pymol/patches/musl.patch
diff --git a/srcpkgs/pymol/patches/musl.patch b/srcpkgs/pymol/patches/musl.patch
new file mode 100644
index 00000000000..a94d8235593
--- /dev/null
+++ b/srcpkgs/pymol/patches/musl.patch
@@ -0,0 +1,13 @@
+diff --git a/ov/src/ov_types.h b/ov/src/ov_types.h
+index 6d2ad80..11d1589 100644
+--- ov/src/ov_types.h
++++ ov/src/ov_types.h
+@@ -19,6 +19,8 @@ extern "C" {
+ #include <windows.h>
+ #endif
+
++#include <cstddef>
++
+ /* automatically detect 64-bit machines */
+
+ #ifndef OV_32_BIT
diff --git a/srcpkgs/pymol/template b/srcpkgs/pymol/template
index 466f6d09db0..426973109ec 100644
--- a/srcpkgs/pymol/template
+++ b/srcpkgs/pymol/template
@@ -1,7 +1,7 @@
# Template file for 'pymol'
pkgname=pymol
version=2.3.0
-revision=3
+revision=4
wrksrc=${pkgname}-open-source-${version}
build_style="python3-module"
hostmakedepends="python3"
@@ -18,9 +18,10 @@ checksum="62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0
0ea81faaf336becc669a193777d0dca55475d303d1236b57df25cf67ff7c2bcd"
skip_extraction="${pkgname}.png"
-case $XBPS_TARGET_MACHINE in
- *-musl) broken="segfaults on start";;
-esac
+if [ "$XBPS_TARGET_LIBC" = musl ]; then
+ makedepends+=" libexecinfo-devel"
+ LDFLAGS="-lexecinfo"
+fi
# TODO: make it use pkg-config, if possible
CXXFLAGS="-I${XBPS_CROSS_BASE}/${py3_inc} -I${XBPS_CROSS_BASE}/usr/include/libxml2
@@ -30,4 +31,7 @@ post_install() {
vlicense LICENSE
vinstall "${FILESDIR}/${pkgname}.desktop" 755 usr/share/applications
vinstall "${XBPS_SRCDISTDIR}/${pkgname}-${version}/${pkgname}.png" 644 usr/share/pixmaps
+
+ # these tests are written for python2
+ rm -r "${DESTDIR}/${py3_sitelib}/pymol/pymol_path/test"
}
next reply other threads:[~2020-09-28 20:08 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-09-28 20:08 ericonr [this message]
2020-09-28 20:22 ` [PR PATCH] [Updated] " ericonr
2020-09-28 20:40 ` ericonr
2020-09-28 20:50 ` ericonr
2020-09-28 20:51 ` [PR PATCH] [Merged]: " ericonr
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